# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # # Run this file to update the package using: # source("data-raw/_internals.R") library(dplyr, warn.conflicts = FALSE) devtools::load_all(quiet = TRUE) old_globalenv <- ls(envir = globalenv()) # Save internal data to R/sysdata.rda ------------------------------------- # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv", skip = 10, sep = "\t", stringsAsFactors = FALSE, header = TRUE, strip.white = TRUE, na = c(NA, "", NULL)) %>% # take the order of the reference.rule_group column in the original data file mutate(reference.rule_group = factor(reference.rule_group, levels = unique(reference.rule_group), ordered = TRUE), sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>% arrange(reference.rule_group, reference.version, sorting_rule, reference.rule) %>% mutate(reference.rule_group = as.character(reference.rule_group)) %>% select(-sorting_rule) # Translations TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv", sep = "\t", stringsAsFactors = FALSE, header = TRUE, blank.lines.skip = TRUE, fill = TRUE, strip.white = TRUE, encoding = "UTF-8", fileEncoding = "UTF-8", na.strings = c(NA, "", NULL), allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1" quote = "") # for checking input in `language` argument in e.g. mo_*() and ab_*() functions LANGUAGES_SUPPORTED <- c(Danish = "da", German = "de", English = "en", Spanish = "es", French = "fr", Italian = "it", Dutch = "nl", Portuguese = "pt", Russian = "ru", Swedish = "sv") # EXAMPLE_ISOLATES <- readRDS("data-raw/example_isolates.rds") # vectors of CoNS and CoPS, improves speed in as.mo() create_species_cons_cops <- function(type = c("CoNS", "CoPS")) { # Determination of which staphylococcal species are CoNS/CoPS according to: # - Becker et al. 2014, PMID 25278577 # - Becker et al. 2019, PMID 30872103 # - Becker et al. 2020, PMID 32056452 # this function returns class MO_staph <- AMR::microorganisms MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE] if (type == "CoNS") { MO_staph[which(MO_staph$species %in% c("coagulase-negative", "argensis", "arlettae", "auricularis", "borealis", "caeli", "capitis", "caprae", "carnosus", "casei", "chromogenes", "cohnii", "condimenti", "croceilyticus", "debuckii", "devriesei", "edaphicus", "epidermidis", "equorum", "felis", "fleurettii", "gallinarum", "haemolyticus", "hominis", "jettensis", "kloosii", "lentus", "lugdunensis", "massiliensis", "microti", "muscae", "nepalensis", "pasteuri", "petrasii", "pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus", "pulvereri", "rostri", "saccharolyticus", "saprophyticus", "sciuri", "simulans", "stepanovicii", "succinus", "ureilyticus", "vitulinus", "vitulus", "warneri", "xylosus", "caledonicus", "canis", "durrellii", "lloydii") | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))), "mo", drop = TRUE] } else if (type == "CoPS") { MO_staph[which(MO_staph$species %in% c("coagulase-positive", "coagulans", "agnetis", "argenteus", "cornubiensis", "delphini", "lutrae", "hyicus", "intermedius", "pseudintermedius", "pseudointermedius", "schweitzeri", "simiae", "roterodami") | (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")), "mo", drop = TRUE] } } MO_CONS <- create_species_cons_cops("CoNS") MO_COPS <- create_species_cons_cops("CoPS") MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG") # antibiotic groups # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv) globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab") AB_AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab) AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX")) AB_ANTIFUNGALS <- AB_lookup %>% filter(group %like% "antifungal") %>% pull(ab) AB_ANTIMYCOBACTERIALS <- AB_lookup %>% filter(group %like% "antimycobacterial") %>% pull(ab) AB_CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab) AB_CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab) AB_CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab) AB_CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab) AB_CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab) AB_CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab) AB_CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab) AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"] AB_FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab) AB_GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab) AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela AB_GLYCOPEPTIDES_EXCEPT_LIPO <- AB_GLYCOPEPTIDES[!AB_GLYCOPEPTIDES %in% AB_LIPOGLYCOPEPTIDES] AB_LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab) AB_MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% pull(ab) AB_OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab) AB_PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab) AB_POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab) AB_QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab) AB_STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab) AB_TETRACYCLINES <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab) AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"] AB_TRIMETHOPRIMS <- antibiotics %>% filter(group %like% "trimethoprim") %>% pull(ab) AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ")) AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS) # this will be used for documentation: DEFINED_AB_GROUPS <- ls(envir = globalenv()) DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab] # Export to package as internal data ---- usethis::use_data(EUCAST_RULES_DF, TRANSLATIONS, LANGUAGES_SUPPORTED, # EXAMPLE_ISOLATES, MO_CONS, MO_COPS, MO_STREP_ABCG, AB_AMINOGLYCOSIDES, AB_AMINOPENICILLINS, AB_ANTIFUNGALS, AB_ANTIMYCOBACTERIALS, AB_CARBAPENEMS, AB_CEPHALOSPORINS, AB_CEPHALOSPORINS_1ST, AB_CEPHALOSPORINS_2ND, AB_CEPHALOSPORINS_3RD, AB_CEPHALOSPORINS_4TH, AB_CEPHALOSPORINS_5TH, AB_CEPHALOSPORINS_EXCEPT_CAZ, AB_FLUOROQUINOLONES, AB_LIPOGLYCOPEPTIDES, AB_GLYCOPEPTIDES, AB_GLYCOPEPTIDES_EXCEPT_LIPO, AB_LINCOSAMIDES, AB_MACROLIDES, AB_OXAZOLIDINONES, AB_PENICILLINS, AB_POLYMYXINS, AB_QUINOLONES, AB_STREPTOGRAMINS, AB_TETRACYCLINES, AB_TETRACYCLINES_EXCEPT_TGC, AB_TRIMETHOPRIMS, AB_UREIDOPENICILLINS, AB_BETALACTAMS, DEFINED_AB_GROUPS, internal = TRUE, overwrite = TRUE, version = 2, compress = "xz") # Export data sets to the repository in different formats ----------------- write_md5 <- function(object) { conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5")) writeLines(digest::digest(object, "md5"), conn) close(conn) } changed_md5 <- function(object) { tryCatch({ conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5")) compared <- digest::digest(object, "md5") != readLines(con = conn) close(conn) compared }, error = function(e) TRUE) } # give official names to ABs and MOs rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo)) if (changed_md5(rsi)) { usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('/data-raw/')}")) write_md5(rsi) try(saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(rsi, "data-raw/rsi_translation.sas"), silent = TRUE) try(haven::write_sav(rsi, "data-raw/rsi_translation.sav"), silent = TRUE) try(haven::write_dta(rsi, "data-raw/rsi_translation.dta"), silent = TRUE) try(openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx"), silent = TRUE) } mo <- dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character) if (changed_md5(mo)) { usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('/data-raw/')}")) write_md5(mo) try(saveRDS(mo, "data-raw/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(dplyr::select(mo, -snomed), "data-raw/microorganisms.sas"), silent = TRUE) try(haven::write_sav(dplyr::select(mo, -snomed), "data-raw/microorganisms.sav"), silent = TRUE) try(haven::write_dta(dplyr::select(mo, -snomed), "data-raw/microorganisms.dta"), silent = TRUE) try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE) } if (changed_md5(microorganisms.old)) { usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.old')} to {usethis::ui_value('/data-raw/')}")) write_md5(microorganisms.old) try(saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas"), silent = TRUE) try(haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav"), silent = TRUE) try(haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta"), silent = TRUE) try(openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx"), silent = TRUE) } ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character) if (changed_md5(ab)) { usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('/data-raw/')}")) write_md5(ab) try(saveRDS(ab, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(ab, "data-raw/antibiotics.sas"), silent = TRUE) try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE) try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE) try(openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx"), silent = TRUE) } av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character) if (changed_md5(av)) { usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('/data-raw/')}")) write_md5(av) try(saveRDS(av, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(av, "data-raw/antivirals.sas"), silent = TRUE) try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE) try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE) try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE) } if (changed_md5(intrinsic_resistant)) { usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}")) write_md5(intrinsic_resistant) try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas"), silent = TRUE) try(haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav"), silent = TRUE) try(haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta"), silent = TRUE) try(openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE) } if (changed_md5(dosage)) { usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('/data-raw/')}")) write_md5(dosage) try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE) try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE) try(haven::write_sas(dosage, "data-raw/dosage.sas"), silent = TRUE) try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE) try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE) try(openxlsx::write.xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE) } # remove leftovers from global env current_globalenv <- ls(envir = globalenv()) rm(list = current_globalenv[!current_globalenv %in% old_globalenv]) rm(current_globalenv)